A Toolkit for Flow And Mass Cytometry Data
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Documentation for package ‘CytoTree’ version 1.4.0
Help Pages
| CytoTree-package | Visualization and analyzation for flow cytometry data |
| buildTree | buildTree |
| constraintMatrix | constraintMatrix |
| correctBatchCYT | correctBatchCYT |
| createCYT | create an CYT object |
| CYT | Class 'CYT' |
| CYT-class | Class 'CYT' |
| CYT-class, | Class 'CYT' |
| CYTclass, | Class 'CYT' |
| CytoTree | Visualization and analyzation for flow cytometry data |
| defLeafCells | definition of leaf cells |
| defRootCells | definition of root cells |
| fetchCell | Fetching cellls of CYT |
| fetchClustMeta | Fetching clusters' metadata of CYT |
| fetchPlotMeta | Fetching plot metadata of CYT |
| find_neighbors | K Nearest Neighbour Search |
| gatingMatrix | Apply gating on the matrix data |
| plot2D | Visualization of 2D data of CYT |
| plot3D | Visualization of 3D data of CYT |
| plotBranchHeatmap | Visualization heatmap of branch data of CYT |
| plotCluster | Visualization of cluster data of CYT |
| plotClusterHeatmap | Visualization heatmap of cluster data of CYT |
| plotHeatmap | Visualization heatmap of data of CYT |
| plotMarkerDensity | plotMarkerDensity |
| plotPieCluster | Visualization pie plot of cluster data of CYT |
| plotPieTree | plot MST pie of CYT |
| plotPseudotimeDensity | plot Pseudotime density of CYT |
| plotPseudotimeTraj | plotPseudotimeTraj |
| plotTrajHeatmap | Visualization heatmap of intermediate cells of CYT |
| plotTree | plot MST of CYT |
| plotViolin | Visualization violin plot of CYT |
| processingCluster | processingCluster |
| Rphenograph | RphenoGraph clustering |
| runClara | runClara |
| runCluster | Specific Clustering Method Toolkits |
| runDiff | Calculate differential expression markers |
| runDiffusionMap | Calculate diffusion map in CYT |
| runExprsExtract | Extract the expression data from a FCS file with preprocessing |
| runExprsMerge | Merge the expression matrix from multiple FCS files with preprocessing |
| runFastPCA | Calculate principal components in CYT |
| runHclust | runHclust |
| runKmeans | runKmeans |
| runKNN | Calculate k-nearest neighbors of CYT |
| runMclust | runMclust |
| runPhenograph | RphenoGraph clustering |
| runPseudotime | Calculation of Pseudotime |
| runSOM | calculation SOM in CYT object |
| runTSNE | Calculate t-Distributed Stochastic Neighbor Embedding in CYT |
| runUMAP | Calculating UMAP |
| runWalk | Walk between root cells and leaf cells |
| subsetCYT | subset CYT object |
| updateClustMeta | Update clusters' meta information of CYT |
| updatePlotMeta | Update plot meta information of CYT |